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Cre is an enzyme that is used to cut and paste DNA, an action known as recombination. Thus Cre is called a recombinase (named Causes recombination).

Cut and paste means that there are two recognition sites in DNA, called LoxP sites, and Cre cuts the DNA between the two sites, either removing it entirely or flipping it around.

The FLP-FRT system works in a similar fashion.

Overview Figure